I got the code to work with a consistent combination of mpi and gcc compilers.
Thanks for your help! -Manav > On Mar 11, 2015, at 2:35 PM, Barry Smith <[email protected]> wrote: > > >> On Mar 11, 2015, at 1:50 PM, Manav Bhatia <[email protected]> wrote: >> >> >>> On Mar 11, 2015, at 1:47 PM, Satish Balay <[email protected]> wrote: >>> >>> Actually mumps is being used - so fortran is required [by mumps] >>> >>> The reason for the 'multiple' libgfortran messages is: openmpi is >>> compiled with an older version of gcc/gfortran >>> >> >> You are right about openmpi being build with an older version of the >> compiler. I am trying to mix and match codes. > > This is not a good idea. It is really really difficult for us to help you > get things working when you have mixed and matched codes. > > Barry > >> >>> [and I suspect its harmless - as the binaries are created] >>> >>> The primary issue to check: is this openmpi install functional - if so >>> how do you run mpi binaries? Perhaps its a cluster - and have to go >>> through a scheduler.. [i.e make check is perhaps inappropriate for >>> this case] >> >> This might be true. This is my first time working on this system, so I need >> to find out the details. >> >>> >>> Satish >>> ---------- >>> >>> Python version: >>> 2.4.2 (#1, Jan 10 2008, 17:43:47) >>> [GCC 4.1.2 20070115 (prerelease) (SUSE Linux)] >>> >>> Executing: mpicc --version >>> stdout: >>> gcc (GCC) 4.8.3 >>> >>> Executing: mpicc -show >>> stdout: gcc -I/usr/local/mpi/x86_64/openmpi-1.4.2/include -pthread >>> -L/usr/local/mpi/x86_64/openmpi-1.4.2/lib -lmpi -lopen-rte -lopen-pal -ldl >>> -Wl,--export-dynamic -lnsl -lutil -lm -ldl >>> >>> Driving: /usr/local/gnu/gcc-4.8.3/bin/gfortran -o >>> /tmp/petsc-X1bXQ9/config.compilers/conftest -v -Wall -Wno-unused-variable >>> -ffree-line-length-0 -Wno-unused-dummy-argument -O >>> /tmp/petsc-X1bXQ9/config.compilers/conftest.o >>> -L/usr/local/mpi/x86_64/openmpi-1.4.2/lib >>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc/x86_64-unknown-linux-gnu/4.8.3 >>> -L/usr/local/s\ >>> erver/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc >>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib64 >>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib -ldl -lmpi -lopen-rte >>> -lopen-pal -lnsl -lutil -lgcc_s -lpthread -ldl >>> -I/usr/local/mpi/x86_64/openmpi-1.4.2/include -pthread >>> -I/usr/local/mpi/x86_64/openmpi-1.4.2/lib >>> -L/usr/local/mpi/x86_64/openmpi-1.4.2/lib -lmpi_f90 -lmpi_f77 -lmpi >>> -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -l gfortran >>> -lm -ldl -l gfortran -l m -shared-libgcc >>> -specs=/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib64/libgfortran.spec >>> >>> >>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, needed >>> by /usr/local/mpi/x86_64/openmpi-1.4.2/lib/libmpi_f90.so, may conflict with >>> libgfortran.so.3 >>> >>> >>> >>> On Wed, 11 Mar 2015, Barry Smith wrote: >>> >>>> >>>> Since you are providing mpicc and mpicxx do not provide the >>>> --with-mpi-include= --with-mpi-lib= >>>> >>>> I notice you have --with-fortran=0 if you do not want fortran than use >>>> --with-fc=0 and do not provide --FC and this may solve the gfortran issue >>>> >>>> Barry >>>> >>>> >>>> >>>>> On Mar 11, 2015, at 1:24 PM, Manav Bhatia <[email protected]> wrote: >>>>> >>>>> I apologize for not sending these files along. Here they are for the two >>>>> machines. >>>>> >>>>> Really appreciate your help. >>>>> >>>>> -Manav >>>>> >>>>> >>>>>> On Mar 11, 2015, at 1:21 PM, Barry Smith <[email protected]> wrote: >>>>>> >>>>>> >>>>>> Lots of problems with your system but the biggest is that it appears you >>>>>> have two gfortran installs that interfere with each other. If you had >>>>>> followed the instructions and sent configure.log and make.log we could >>>>>> help you more. >>>>>> >>>>>> Barry >>>>>> >>>>>> >>>>>>> On Mar 11, 2015, at 1:12 PM, Manav Bhatia <[email protected]> wrote: >>>>>>> >>>>>>> Greetings! >>>>>>> >>>>>>> I have come across the following error while running make check. I am >>>>>>> not sure where to begin to sort this out. Any pointers would be greatly >>>>>>> appreciated. >>>>>>> >>>>>>> Talon-login[114] bhatia$ make check >>>>>>> gmake[1]: Entering directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3' >>>>>>> Running test examples to verify correct installation >>>>>>> Using PETSC_DIR=/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3 and >>>>>>> PETSC_ARCH=arch-linux2-cxx-opt >>>>>>> gmake[2]: Entering directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> gmake[2]: Leaving directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> gmake[2]: Entering directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> *******************Error detected during compile or >>>>>>> link!******************* >>>>>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> /cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials >>>>>>> ex19 >>>>>>> ********************************************************************************* >>>>>>> gmake[3]: Entering directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> gmake[4]: Entering directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> gmake[4]: Leaving directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> mpicxx -o ex19.o -c -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>> -Wno-unknown-pragmas -O >>>>>>> -I/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/include >>>>>>> -I/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/arch-linux2-cxx-opt/include >>>>>>> -I/usr/local/openssl/x86_64/include >>>>>>> -I/usr/local/mpi/x86_64/openmpi/include >>>>>>> -I/usr/local/mpi/x86_64/openmpi-1.4.2/include `pwd`/ex19.c >>>>>>> mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>> -O -o ex19 ex19.o >>>>>>> -L/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/arch-linux2-cxx-opt/lib >>>>>>> -lpetsc >>>>>>> -Wl,-rpath,/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/arch-linux2-cxx-opt/lib >>>>>>> -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack >>>>>>> -lsuperlu_4.3 -lsuperlu_dist_3.3 >>>>>>> -Wl,-rpath,/cavs/projects/sams/codes/raptor/lapack >>>>>>> -L/cavs/projects/sams/codes/raptor/lapack -llapack >>>>>>> -Wl,-rpath,/cavs/projects/sams/codes/raptor/blas >>>>>>> -L/cavs/projects/sams/codes/raptor/blas -lblas -lparmetis -lmetis >>>>>>> -lpthread -Wl,-rpath,/usr/local/openssl/x86_64/lib >>>>>>> -L/usr/local/openssl/x86_64/lib -lssl -lcrypto >>>>>>> -Wl,-rpath,/usr/local/mpi/x86_64/openmpi/lib >>>>>>> -L/usr/local/mpi/x86_64/openmpi/lib -lmpi_cxx -lmpi >>>>>>> -L/usr/local/mpi/x86_64/openmpi-1.4.2/lib >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc/x86_64-unknown-linux-gnu/4.8.3 >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib64 >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib -lmpi_f90 -lmpi_f77 >>>>>>> -lgfortran -lm -lgfortran -lm -lgfortran -lm -lquadmath -lm -lmpi_cxx >>>>>>> -lstdc++ -L/usr/local/mpi/x86_64/openmpi-1.4.2/lib >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc/x86_64-unknown-linux-gnu/4.8.3 >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib64 >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib -ldl -lmpi >>>>>>> -lopen-rte -lopen-pal -lnsl -lutil -lgcc_s -lpthread -ldl >>>>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, >>>>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict >>>>>>> with libgfortran.so.3 >>>>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, >>>>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict >>>>>>> with libgfortran.so.3 >>>>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, >>>>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict >>>>>>> with libgfortran.so.3 >>>>>>> /bin/rm -f ex19.o >>>>>>> gmake[3]: Leaving directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 >>>>>>> MPI process >>>>>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes. >>>>>>> This will severely limit memory registrations. >>>>>>> libibverbs: Warning: couldn't open config directory '/etc/libibverbs.d'. >>>>>>> libibverbs: Warning: no userspace device-specific driver found for >>>>>>> /sys/class/infiniband_verbs/uverbs0 >>>>>>> CMA: unable to open /dev/infiniband/rdma_cm >>>>>>> libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes. >>>>>>> This will severely limit memory registrations. >>>>>>> libibverbs: Warning: couldn't open config directory '/etc/libibverbs.d'. >>>>>>> [Talon-login:18281] *** Process received signal *** >>>>>>> [Talon-login:18281] Signal: Segmentation fault (11) >>>>>>> [Talon-login:18281] Signal code: Address not mapped (1) >>>>>>> [Talon-login:18281] Failing at address: 0x100002990 >>>>>>> [Talon-login:18281] [ 0] /lib64/libpthread.so.0 [0x2b8e9cbc6c00] >>>>>>> [Talon-login:18281] [ 1] /usr/ofed/lib64/libibverbs.so.1 >>>>>>> [0x2b8e9fcad4ce] >>>>>>> [Talon-login:18281] [ 2] >>>>>>> /usr/ofed/lib64/libibverbs.so.1(ibv_get_device_list+0x9e) >>>>>>> [0x2b8e9fcac49e] >>>>>>> [Talon-login:18281] [ 3] >>>>>>> /usr/local/mpi/x86_64/openmpi-1.4.2/lib/openmpi/mca_btl_openib.so >>>>>>> [0x2b8e9fdbe15a] >>>>>>> [Talon-login:18281] [ 4] >>>>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(mca_btl_base_select+0x156) >>>>>>> [0x2b8e9d223166] >>>>>>> [Talon-login:18281] [ 5] >>>>>>> /usr/local/mpi/x86_64/openmpi-1.4.2/lib/openmpi/mca_bml_r2.so >>>>>>> [0x2b8e9f997821] >>>>>>> [Talon-login:18281] [ 6] >>>>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(mca_bml_base_init+0x72) >>>>>>> [0x2b8e9d222972] >>>>>>> [Talon-login:18281] [ 7] >>>>>>> /usr/local/mpi/x86_64/openmpi-1.4.2/lib/openmpi/mca_pml_ob1.so >>>>>>> [0x2b8e9f77fc8f] >>>>>>> [Talon-login:18281] [ 8] >>>>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(mca_pml_base_select+0x383) >>>>>>> [0x2b8e9d22c743] >>>>>>> [Talon-login:18281] [ 9] /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0 >>>>>>> [0x2b8e9d1f0050] >>>>>>> [Talon-login:18281] [10] >>>>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(PMPI_Init_thread+0xc1) >>>>>>> [0x2b8e9d20db41] >>>>>>> [Talon-login:18281] [11] ./ex19(PetscInitialize+0x1bd) [0x4990fe] >>>>>>> [Talon-login:18281] [12] ./ex19(main+0x2a) [0x48471e] >>>>>>> [Talon-login:18281] [13] /lib64/libc.so.6(__libc_start_main+0xf4) >>>>>>> [0x2b8e9e331164] >>>>>>> [Talon-login:18281] [14] ./ex19 [0x482639] >>>>>>> [Talon-login:18281] *** End of error message *** >>>>>>> -------------------------------------------------------------------------- >>>>>>> mpirun noticed that process rank 0 with PID 18281 on node >>>>>>> Talon-login.HPC.MsState.Edu exited on signal 11 (Segmentation fault). >>>>>>> -------------------------------------------------------------------------- >>>>>>> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 >>>>>>> MPI processes >>>>>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes. >>>>>>> This will severely limit memory registrations. >>>>>>> libibverbs: Warning: couldn't open config directory '/etc/libibverbs.d'. >>>>>>> libibverbs: Warning: no userspace device-specific driver found for >>>>>>> /sys/class/infiniband_verbs/uverbs0 >>>>>>> CMA: unable to open /dev/infiniband/rdma_cm >>>>>>> libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes. >>>>>>> This will severely limit memory registrations. >>>>>>> libibverbs: Warning: couldn't open config directory '/etc/libibverbs.d'. >>>>>>> [Talon-login:18286] *** Process received signal *** >>>>>>> [Talon-login:18286] Signal: Segmentation fault (11) >>>>>>> [Talon-login:18286] Signal code: Address not mapped (1) >>>>>>> [Talon-login:18286] Failing at address: 0x100002990 >>>>>>> [Talon-login:18286] [ 0] /lib64/libpthread.so.0 [0x2acc0604ec00] >>>>>>> [Talon-login:18286] [ 1] /usr/ofed/lib64/libibverbs.so.1 >>>>>>> [0x2acc091354ce] >>>>>>> [Talon-login:18286] [ 2] >>>>>>> /usr/ofed/lib64/libibverbs.so.1(ibv_get_device_list+0x9e) >>>>>>> [0x2acc0913449e] >>>>>>> [Talon-login:18286] [ 3] >>>>>>> /usr/local/mpi/x86_64/openmpi-1.4.2/lib/openmpi/mca_btl_openib.so >>>>>>> [0x2acc0924615a] >>>>>>> [Talon-login:18286] [ 4] >>>>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(mca_btl_base_select+0x156) >>>>>>> [0x2acc066ab166] >>>>>>> [Talon-login:18286] [ 5] >>>>>>> /usr/local/mpi/x86_64/openmpi-1.4.2/lib/openmpi/mca_bml_r2.so >>>>>>> [0x2acc08e1f821] >>>>>>> [Talon-login:18286] [ 6] >>>>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(mca_bml_base_init+0x72) >>>>>>> [0x2acc066aa972] >>>>>>> [Talon-login:18286] [ 7] >>>>>>> /usr/local/mpi/x86_64/openmpi-1.4.2/lib/openmpi/mca_pml_ob1.so >>>>>>> [0x2acc08c07c8f] >>>>>>> [Talon-login:18286] [ 8] >>>>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(mca_pml_base_select+0x383) >>>>>>> [0x2acc066b4743] >>>>>>> [Talon-login:18286] [ 9] /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0 >>>>>>> [0x2acc06678050] >>>>>>> [Talon-login:18286] [10] >>>>>>> /usr/local/mpi/x86_64/openmpi/lib/libmpi.so.0(PMPI_Init_thread+0xc1) >>>>>>> [0x2acc06695b41] >>>>>>> [Talon-login:18286] [11] ./ex19(PetscInitialize+0x1bd) [0x4990fe] >>>>>>> [Talon-login:18286] [12] ./ex19(main+0x2a) [0x48471e] >>>>>>> [Talon-login:18286] [13] /lib64/libc.so.6(__libc_start_main+0xf4) >>>>>>> [0x2acc077b9164] >>>>>>> [Talon-login:18286] [14] ./ex19 [0x482639] >>>>>>> [Talon-login:18286] *** End of error message *** >>>>>>> -------------------------------------------------------------------------- >>>>>>> mpirun noticed that process rank 0 with PID 18286 on node >>>>>>> Talon-login.HPC.MsState.Edu exited on signal 11 (Segmentation fault). >>>>>>> -------------------------------------------------------------------------- >>>>>>> gmake[3]: Entering directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> gmake[3]: Leaving directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> gmake[2]: Leaving directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> gmake[2]: Entering directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> *******************Error detected during compile or >>>>>>> link!******************* >>>>>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> /cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials >>>>>>> ex5f >>>>>>> ********************************************************* >>>>>>> gmake[3]: Entering directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> mpif90 -c -Wall -Wno-unused-variable -ffree-line-length-0 >>>>>>> -Wno-unused-dummy-argument -O >>>>>>> -I/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/include >>>>>>> -I/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/arch-linux2-cxx-opt/include >>>>>>> -I/usr/local/openssl/x86_64/include >>>>>>> -I/usr/local/mpi/x86_64/openmpi/include >>>>>>> -I/usr/local/mpi/x86_64/openmpi-1.4.2/include -o ex5f.o ex5f.F >>>>>>> mpif90 -Wall -Wno-unused-variable -ffree-line-length-0 >>>>>>> -Wno-unused-dummy-argument -O -o ex5f ex5f.o >>>>>>> -L/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/arch-linux2-cxx-opt/lib >>>>>>> -lpetsc >>>>>>> -Wl,-rpath,/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/arch-linux2-cxx-opt/lib >>>>>>> -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack >>>>>>> -lsuperlu_4.3 -lsuperlu_dist_3.3 >>>>>>> -Wl,-rpath,/cavs/projects/sams/codes/raptor/lapack >>>>>>> -L/cavs/projects/sams/codes/raptor/lapack -llapack >>>>>>> -Wl,-rpath,/cavs/projects/sams/codes/raptor/blas >>>>>>> -L/cavs/projects/sams/codes/raptor/blas -lblas -lparmetis -lmetis >>>>>>> -lpthread -Wl,-rpath,/usr/local/openssl/x86_64/lib >>>>>>> -L/usr/local/openssl/x86_64/lib -lssl -lcrypto >>>>>>> -Wl,-rpath,/usr/local/mpi/x86_64/openmpi/lib >>>>>>> -L/usr/local/mpi/x86_64/openmpi/lib -lmpi_cxx -lmpi >>>>>>> -L/usr/local/mpi/x86_64/openmpi-1.4.2/lib >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc/x86_64-unknown-linux-gnu/4.8.3 >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4..8.3/lib64 >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib -lmpi_f90 -lmpi_f77 >>>>>>> -lgfortran -lm -lgfortran -lm -lgfortran -lm -lquadmath -lm -lmpi_cxx >>>>>>> -lstdc++ -L/usr/local/mpi/x86_64/openmpi-1.4.2/lib >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc/x86_64-unknown-linux-gnu/4.8.3 >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib/gcc >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib64 >>>>>>> -L/usr/local/server/x86_64-SuSE10/gnu/gcc-4.8.3/lib -ldl -lmpi >>>>>>> -lopen-rte -lopen-pal -lnsl -lutil -lgcc_s -lpthread -ldl >>>>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, >>>>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict >>>>>>> with libgfortran.so.3 >>>>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, >>>>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict >>>>>>> with libgfortran.so.3 >>>>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, >>>>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict >>>>>>> with libgfortran.so.3 >>>>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, >>>>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict >>>>>>> with libgfortran.so.3 >>>>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, >>>>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict >>>>>>> with libgfortran.so.3 >>>>>>> /usr/local/gnu/gcc-4.8.3/binutils/bin/ld: warning: libgfortran.so.1, >>>>>>> needed by /usr/local/mpi/x86_64/openmpi/lib/libmpi_f90.so, may conflict >>>>>>> with libgfortran.so.3 >>>>>>> /bin/rm -f ex5f.o >>>>>>> gmake[3]: Leaving directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> Possible error running Fortran example src/snes/examples/tutorials/ex5f >>>>>>> with 1 MPI process >>>>>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes. >>>>>>> This will severely limit memory registrations. >>>>>>> libibverbs: Warning: couldn't open config directory '/etc/libibverbs.d'. >>>>>>> libibverbs: Warning: no userspace device-specific driver found for >>>>>>> /sys/class/infiniband_verbs/uverbs0 >>>>>>> CMA: unable to open /dev/infiniband/rdma_cm >>>>>>> libibverbs: Warning: RLIMIT_MEMLOCK is 32768 bytes. >>>>>>> This will severely limit memory registrations. >>>>>>> libibverbs: Warning: couldn't open config directory '/etc/libibverbs.d'. >>>>>>> >>>>>>> Program received signal SIGSEGV: Segmentation fault - invalid memory >>>>>>> reference. >>>>>>> >>>>>>> Backtrace for this error: >>>>>>> #0 0x2B6CD4A6F4D7 >>>>>>> #1 0x2B6CD4A6FADE >>>>>>> #2 0x2B6CD5805E1F >>>>>>> #3 0x2B6CD716F4CE >>>>>>> #4 0x2B6CD716E49D >>>>>>> #5 0x2B6CD7280159 >>>>>>> #6 0x2B6CD46E5165 >>>>>>> #7 0x2B6CD6E59820 >>>>>>> #8 0x2B6CD46E4971 >>>>>>> #9 0x2B6CD6C41C8E >>>>>>> #10 0x2B6CD46EE742 >>>>>>> #11 0x2B6CD46B204F >>>>>>> #12 0x2B6CD46CF99F >>>>>>> #13 0x2B6CD494AA84 >>>>>>> #14 0x489A6D in petscinitialize_ >>>>>>> #15 0x487CEC in MAIN__ at ex5f.F:? >>>>>>> -------------------------------------------------------------------------- >>>>>>> mpirun noticed that process rank 0 with PID 18354 on node >>>>>>> Talon-login.HPC.MsState.Edu exited on signal 11 (Segmentation fault). >>>>>>> -------------------------------------------------------------------------- >>>>>>> gmake[3]: Entering directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> gmake[3]: Leaving directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> gmake[2]: Leaving directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> gmake[2]: Entering directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> gmake[2]: Leaving directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3/src/snes/examples/tutorials' >>>>>>> Completed test examples >>>>>>> gmake[1]: Leaving directory >>>>>>> `/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3' >>>>>>> ========================================= >>>>>>> Now to evaluate the computer systems you plan use - do: >>>>>>> make PETSC_DIR=/cavs/projects/sams/codes/raptor/petsc/petsc-3.5.3 >>>>>>> PETSC_ARCH=arch-linux2-cxx-opt streams NPMAX=<number of MPI processes >>>>>>> you intend to use> >>>>>>> Talon-login[115] bhatia$ >>>>>>> >>>>>>> >>>>>>> Thanks, >>>>>>> Manav >>>>>>> >>>>>> >>>>> >>>>> <configure_shadow.log><configure_talon.log><make_shadow.log><make_talon.log> >>>> >>>> >> >
